Local histories suggest that a church was built in Smailholm in the twelfth century. Unfortunately very little evidence remains of this Norman church. However records show that in 1171 Smailholm was a dependent of Earlston church. It was presented by Walter Olifond (d. 1242) to the Coldingham monks in exchange for vicars. The church was dedicated in1253 by David de Bernham, Bishop of St Andrews.From 1408 until the Reformation in Scotland (1560) Smailholm church was in the in the possession of Dryburgh Abbey. During the sixteenth century the church was one of several places of refuge during the English raids on the Border villages.
From 1632 onwards the church was extensively rebuilt on the site of the original church. There were further alterations in 1820 resulting in the church that exists today. The apsidal addition to the north, containing the vestry, was probably added at that time. The interior of the church was altered during the twentieth century.
The church has a number of interesting features that include a boarded vaulted roof and a Laird’s loft (the Haddington Loft) accessible by means of external stairs at the north west end that continue in the building. Also there are stained glass windows in the east end of the chancel depicting St Cuthbert (who is believed to been born in the area) and St Giles. These were installed in 1907 to the memory of Sir Walter Scott whose grandfather farmed the near-by Sandyknowes Farm.